Spades Genome Assembly

Question

[Umer]

Hi Reader,

I am using SPAdes 4.0.0 to assemble some fungal genomes from Illumina short read PE150 data.

My data is at 100x coverage. and i used the following command to run spades

spades.py -k 21 33 55 77 99 111 127 --isolate -1 ILL01_trim_1.fq.gz -2 ILL01_trim_2.fq.gz -t 48 -o ./ILL01/

the log file of assembly looks like this at start

System information:
  SPAdes version: 4.0.0
  Python version: 3.13.0
  OS: Linux-4.18.0-425.13.1.el8_7.x86_64-x86_64-with-glibc2.28

Output dir: /vast/ti78qem/assemblies/spades_assembly/ILL01
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
  Isolate mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/4.ill_trimmed_data/ILL01/ILL01_trim_1.fq.gz']
      right reads: ['/4.ill_trimmed_data/ILL01/ILL01_trim_2.fq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: [21, 33, 55, 77, 99, 111, 127]
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
  Assembly graph output will use GFA v1.2 format
Other parameters:
  Dir for temp files: /spades_assembly/ILL01/tmp
  Threads: 48
  Memory limit (in Gb): 250

My concern is about the line Mode: ONLY assembling (without read error correction).

Isn't this the default behavior of Spades to perform read-error-correction then assamble the reads ?

Another question: At 100x coverage, is it recomended to perform read-errror-correction or not from assaembling the genome ?

thank you.

[dthorbur]

I assume this is a similar issue to this post. The --isolate flag expects high coverage and quality input data that may not require error correction, so I believe this step is skipped when using this flag. Try removing it and seeing what happens.